TY - CHAP
T1 - Proximity-CLIP provides a snapshot of protein-occupied RNA elements at subcellular resolution and transcriptome-wide scale
AU - Benhalevy, Daniel
AU - Hafner, Markus
N1 - Publisher Copyright:
© Springer Science+Business Media, LLC, part of Springer Nature 2020.
PY - 2020
Y1 - 2020
N2 - The distribution of messenger RNAs (mRNAs) to specific subcellular locations has been studied for the past two decades. Technically, studies of RNA localization are lagging those related to protein localization. Here we provide a detailed protocol for Proximity-CLIP, a method recently developed by our group, that combines proximity biotinylation of proteins with photoactivatable ribonucleoside-enhanced protein-RNA cross-linking to simultaneously profile the proteome including RNA-binding proteins (RBPs) and the RBP-bound transcriptome in any given subcellular compartment. The approach is fractionation independent and also enables studying localized RNA-processing intermediates, as well as the identification of regulatory cis-acting elements on RNAs occupied by proteins in a cellular compartment-specific manner.
AB - The distribution of messenger RNAs (mRNAs) to specific subcellular locations has been studied for the past two decades. Technically, studies of RNA localization are lagging those related to protein localization. Here we provide a detailed protocol for Proximity-CLIP, a method recently developed by our group, that combines proximity biotinylation of proteins with photoactivatable ribonucleoside-enhanced protein-RNA cross-linking to simultaneously profile the proteome including RNA-binding proteins (RBPs) and the RBP-bound transcriptome in any given subcellular compartment. The approach is fractionation independent and also enables studying localized RNA-processing intermediates, as well as the identification of regulatory cis-acting elements on RNAs occupied by proteins in a cellular compartment-specific manner.
KW - RNA localization
KW - RNA regulatory elements
KW - RNA-processing intermediates
KW - RNA-protein interactions
KW - Subcellular RNA biology
UR - http://www.scopus.com/inward/record.url?scp=85088681646&partnerID=8YFLogxK
U2 - 10.1007/978-1-0716-0712-1_17
DO - 10.1007/978-1-0716-0712-1_17
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C2 - 32710416
AN - SCOPUS:85088681646
T3 - Methods in Molecular Biology
SP - 283
EP - 305
BT - Methods in Molecular Biology
PB - Humana Press Inc.
ER -